The apparent isomer effect on charge transfer processes in collisions of the ground-state C+ ions with allene and propyne, which have the same C3H4 molecular chemical notation, has been observed experimentally in the collision energy from 0.2 to 4.5 keV. The difference in total charge transfer cross sections between the two isomers was found to be 32% at 0.2 keV, although it decreases to 10% at 4.5 keV. This difference is out of experimental uncertainty of 14.6% at least below the collision energy of 0.5 keV and should be regarded as a real isomer effect. Theoretical analysis based on a molecular orbital expansion method has also confirmed the experimental finding and provided the rationale.